Fast lateral proton migration along membranes is of vital importance for cellular energy homeostasis and various proton-coupled transport processes. It can only occur if attractive forces keep the proton at the interface. How to reconcile this high affinity to the membrane surface with high proton mobility is unclear. Here, we tested whether a minimalistic model interface between an apolar hydrophobic phase (n-decane) and an aqueous phase mimics the biological pathway for lateral proton migration. The observed diffusion span, on the order of tens of micrometers, and the high proton mobility were both similar to the values previously reported for lipid bilayers. Extensive ab initio simulations on the same water∕n-decane interface reproduced the experimentally derived free energy barrier for the excess proton. The free energy profile G H þ adopts the shape of a well at the interface, having a width of two water molecules and a depth of 6 AE 2RT . The hydroniums in direct contact with n-decane have a reduced mobility. However, the hydroniums in the second layer of water molecules are mobile. Their in silico diffusion coefficient matches that derived from our in vitro experiments, ð5.7 AE 0.7Þ × 10 −5 cm 2 s −1 . Conceivably, these are the protons that allow for fast diffusion along biological membranes.hydrophobic liquid | hydrophilic liquid interface | surface acidity | free energy calculations

Self-association of two hydrophobic alpha-helices is studied via unrestrained Monte Carlo (MC) simulations in a hydrophobic slab described by an effective potential. The system under study represents two transmembrane (TM) segments of human glycophorin A (GpA), which form homo-dimers in membranes. The influence of TM electrostatic potential, thickness and hydrophobicity degree of lipid bilayer is investigated. It is shown that the membrane environment stabilizes alpha-helical conformation of GpA monomers, induces their TM insertion and facilitates inter-helical contacts. Head-to-head orientation of the helices is promoted by the voltage difference across the membrane. Subsequent "fine-tuned" assembling of the dimer is mediated by van der Waals interactions. Only the models of dimer, calculated in a hydrophobic slab with applied voltage agree with experimental data, while simulations in vacuo or without TM voltage fail to give reasonable results. The moderate structural heterogeneity of GpA dimers (existence of several groups of states with close energies) is proposed to reflect their equilibrium dynamics in membrane-mimics. The calculations performed for GpA mutants G83A and G86L permit rationalization of mutagenesis data for them. The results of Monte Carlo simulations critically depend on the parameters of the membrane model: adequate description of helix association is achieved in the water-cyclohexane-water system with the membrane thickness 30-34 A, while in membranes with different hydrophobicities and thickness unrealistic conformations of the dimer are found. The computational approach permits efficient prediction of TM helical oligomers based solely on the sequences of interacting peptides.

BNIP3 is a mitochondrial 19-kDa proapoptotic protein, a member of the Bcl-2 family. It has a single COOH-terminal transmembrane (TM) alpha-helical domain, which is required for membrane targeting, proapoptotic activity, hetero- and homo-dimerization in membrane. The role and the molecular details of association of TM helices of BNIP3 are yet to be established. Here, we present a molecular modeling study of helix interactions in its membrane domain. The approach combines Monte Carlo conformational search in an implicit hydrophobic slab followed by molecular dynamics simulations in a hydrated full-atom lipid bilayer. The former technique was used for exhaustive sampling of the peptides' conformational space and for generation of putative "native-like" structures of the dimer. The latter ones were taken as realistic starting points to assess stability and dynamic behavior of the complex in explicit lipid-water surrounding. As a result, several groups of tightly packed right-handed structures of the dimer were proposed. They have almost similar helix-helix interface, which includes the motif A(176)xxxG(180)xxxG(184) and agrees well with previous mutagenesis data and preliminary NMR analysis. Molecular dynamics simulations of these structures reveal perfect adaptation of most of them to heterogeneous membrane environment. A remarkable feature of the predicted dimeric structures is the occurrence of a cluster of H-bonded histidine 173 and serines 168 and 172 on the helix interface, near the N-terminus. Because of specific polar interactions between the monomers, this part of the dimer has no such dense packing as the C-terminal one, thus allowing penetration of water from the extramembrane side into the membrane interior. We propose that the ionization state of His(173) can mediate structural and dynamic properties of the dimer. This, in turn, may be related to pH-dependent proapoptotic activity of BNIP3, which is triggering on by acidosis appearing under hypoxic conditions.

We describe one of the first attempts at unrestrained modeling of self-association of α-helices in implicit heterogeneous membrane-mimic media. The computational approach is based on the Monte Carlo conformational search for peptides in dihedral angles space. The membrane is approximated by an effective potential. The method is tested in calculations of two hydrophobic segments of human glycophorin A (GpA), known to form membrane-spanning dimers in real lipid bilayers. Our main findings may be summarized as follows. Modeling in vacuo does not adequately describe the behavior of GpA helices, failing to reproduce experimental structural data. The membrane environment stabilizes α-helical conformation of GpA monomers, inducing their transmembrane insertion and facilitating interhelical contacts. The voltage difference across the membrane promotes "head-to-head" orientation of the helices. "Fine-tuning" of the monomers in a complex is shown to be regulated by van der Waals interactions. Detailed exploration of conformational space of the system starting from arbitrary locations of two noninteracting helices reveals only several groups of energetically favorable structures. All of them represent tightly packed transmembrane helical dimers. In overall, they agree reasonably well with mutagenesis data, some of them are close to NMR-derived structures. A possibility of left-handed dimers is discussed. We assume that the observed moderate structural heterogeneity (the existence of several groups of states with close energies) reflects a real equilibrium dynamics of the monomers [Formula: see text] at least in membrane mimics used in experimental studies of GpA. The elaborated computational approach is universal and may be employed in studies of a wide class of membrane peptides and proteins.